mvGST

DOI: 10.18129/B9.bioc.mvGST    

Multivariate and directional gene set testing

Bioconductor version: Release (3.6)

mvGST provides platform-independent tools to identify GO terms (gene sets) that are differentially active (up or down) in multiple contrasts of interest. Given a matrix of one-sided p-values (rows for genes, columns for contrasts), mvGST uses meta-analytic methods to combine p-values for all genes annotated to each gene set, and then classify each gene set as being significantly more active (1), less active (-1), or not significantly differentially active (0) in each contrast of interest. With multiple contrasts of interest, each gene set is assigned to a profile (across contrasts) of differential activity. Tools are also provided for visualizing (in a GO graph) the gene sets classified to a given profile.

Author: John R. Stevens and Dennis S. Mecham

Maintainer: John R. Stevens <john.r.stevens at usu.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("mvGST")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("mvGST")

 

PDF	R Script	mvGST Tutorial Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GO, GeneSetEnrichment, GraphAndNetwork, Microarray, OneChannel, Pathways, RNASeq, Software
Version	1.12.2
In Bioconductor since	BioC 3.0 (R-3.1) (3.5 years)
License	GPL-3
Depends	R (>= 2.10.0), GO.db, Rgraphviz
Imports	gProfileR, stringr, topGO, GOstats, annotate, AnnotationDbi, graph
LinkingTo
Suggests	hgu133plus2.db, org.Hs.eg.db
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	mvGST_1.12.2.tar.gz
Windows Binary	mvGST_1.12.2.zip
Mac OS X 10.11 (El Capitan)	mvGST_1.12.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mvGST
Package Short Url	http://bioconductor.org/packages/mvGST/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive